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comparison query.py @ 19:7f712cc0d3d5 draft

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Uploaded 20190304.2
author fabio
date Mon, 04 Mar 2019 08:31:28 -0500
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children c619ad82600e
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18:be864d79c9c7 19:7f712cc0d3d5
1 #!/usr/bin/env python
2
3 import sys, os, optparse, shutil
4
5 __version__ = "1.0.0"
6 VALID_CHARS = '.-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ'
7 # in the case of collections, exitcodes equal to 0 and 1 are not considered errors
8 ERR_EXIT_CODE = 2
9 OK_EXIT_CODE = 0
10
11 def printLog( logfilepath, message, exitcode=OK_EXIT_CODE, exit=False ):
12 print message
13 with open( logfilepath, 'a+' ) as out:
14 out.write( message + '\n' )
15 if exit:
16 sys.exit( exitcode )
17
18 def querySBT( options, args ):
19 output_dir_path = options.outputdir
20 outlogfile = options.outfile
21
22 tree_file_paths = options.treep.split( ',' )
23 tree_file_names = options.treen.split( ',' )
24 tree_def_filepath = None
25 leafnames_filepath = None
26 for idx, tree_file_name in enumerate( tree_file_names ):
27 if tree_file_name == 'howde':
28 tree_def_filepath = tree_file_paths[ idx ]
29 elif tree_file_name == 'leafnames':
30 leafnames_filepath = tree_file_paths[ idx ]
31 if tree_def_filepath is not None and leafnames_filepath is not None:
32 break
33
34 if tree_def_filepath is not None and leafnames_filepath is not None:
35 leafnames_counter = 0
36 with open( leafnames_filepath ) as leafnames_file:
37 for line in leafnames_file:
38 if line.strip():
39 leafnames_counter += 1
40 if leafnames_counter > 0:
41 printLog( outlogfile, 'The selected collection contains a valid tree' )
42 shutil.copyfile( tree_def_filepath, 'howde.txt' )
43 tree_def_filepath = 'howde.txt'
44 for idx, tree_file_name in enumerate( tree_file_names ):
45 if tree_file_name.endswith( 'detbrief.rrr' ):
46 shutil.copyfile( tree_file_paths[ idx ], tree_file_name + '.bf' )
47
48 printLog( outlogfile, 'Creating batch of queries' )
49 # create tmp batch file
50 batch_file_name = 'queries.fa'
51 batch_file = open( batch_file_name, 'w' )
52
53 comma_sep_file_paths = options.files
54 # check if options.files contains at least one file path
55 if comma_sep_file_paths is not None:
56 # split file paths
57 file_paths = comma_sep_file_paths.split(",")
58 # split file names
59 file_names = options.names.split(",")
60 for idx, file_path in enumerate(file_paths):
61 fixed_file_name = ''.join( c for c in file_names[ idx ] if c in VALID_CHARS )
62 printLog( outlogfile, '> processing file ' + file_names[ idx ] + ' ( fixed_name=\"' + fixed_file_name + '\" ) ' )
63 with open(file_path, 'r') as content_file:
64 for line in content_file:
65 line = line.strip()
66 if line:
67 line_split = line.strip().split("\t") # split on tab
68 if len(line_split) == 2: # 0:id , 1:seq , otherwise skip line
69 original_seq_id = line_split[0]
70 # fix seq_id using valid chars only
71 seq_id = ''.join( c for c in original_seq_id if c in VALID_CHARS )
72 printLog( outlogfile, '> sequence ' + original_seq_id + ' ( fixed_name=\"' + seq_id + '\" )' )
73 seq_text = line_split[1]
74
75 # write on batch file
76 batch_file.write( '> ' + fixed_file_name + '_' + seq_id + '\n' + seq_text + '\n' )
77 batch_file.close()
78 # query the tree
79 printLog( outlogfile, 'Querying the tree' )
80 query_res_file_path = os.path.abspath( 'answer.txt' )
81 sort_param = '--sort'
82 if options.sort == 0:
83 sort_param = ''
84 query_exitcode = os.system( 'howdesbt query --tree=' + os.path.abspath( tree_def_filepath ) + ' ' + os.path.abspath( batch_file_name ) + '=' + str(options.threshold) + ' --out=' + query_res_file_path ) + ' ' + sort_param
85 if query_exitcode > 0:
86 printLog( outlogfile, '> ERROR: an error has occurred while querying the tree with the sequence [id: ' + seq_id + '] in input file ' + file_names[ idx ] )
87 else:
88 if os.path.exists( query_res_file_path ):
89 with open( query_res_file_path ) as query_res_file:
90 file_path = ''
91 theta_matches = 0
92 for line in query_res_file:
93 line = line.strip()
94 if line:
95 if line.startswith( '*' ):
96 line_split = line.split( ' ' )
97 theta_matches = int( line_split[ 1 ] )
98 file_name = line_split[ 0 ].replace( '*', '' )
99 file_path = os.path.join( output_dir_path, file_name + '_txt' )
100 open( file_path, 'a' ).close()
101 else:
102 res_file = open( file_path, 'a+' )
103 fraction = str( theta_matches ) + '/' + str( leafnames_counter )
104 score = format( round( float( theta_matches ) / float( leafnames_counter ) , 6 ), '6f' )
105 res_file.write( line + '\t' + fraction + '\t' + score + '\n' )
106 res_file.close()
107 else:
108 printLog( outlogfile, 'An error has occurred while querying the tree', exitcode=ERR_EXIT_CODE, exit=True )
109 else:
110 printLog( outlogfile, 'The selected collection does not contain a valid tree', exitcode=ERR_EXIT_CODE, exit=True )
111 else:
112 printLog( outlogfile, 'The selected collection does not contain a valid tree', exitcode=ERR_EXIT_CODE, exit=True )
113
114 def __main__():
115 # Parse the command line options
116 usage = "Usage: query.py --files comma_sep_file_paths --names comma_seq_file_names --sequences sequences_text --search search_mode --exact exact_alg --sthreshold threshold --outputdir output_dir_path"
117 parser = optparse.OptionParser(usage = usage)
118 parser.add_option("-v", "--version", action="store_true", dest="version",
119 default=False, help="display version and exit")
120 parser.add_option("-f", "--files", type="string",
121 action="store", dest="files", help="comma separated files path")
122 parser.add_option("-n", "--names", type="string",
123 action="store", dest="names", help="comma separated names associated to the files specified in --files")
124 parser.add_option("-k", "--treep", type="string",
125 action="store", dest="treep", help="paths of files in collection")
126 parser.add_option("-m", "--treen", type="string",
127 action="store", dest="treen", help="names of files in collection")
128 parser.add_option("-t", "--threshold", type="float", default=0.7,
129 action="store", dest="threshold", help="search threshold")
130 parser.add_option("-s", "--sort", type="int", default=1,
131 action="store", dest="sort", help="sort results")
132 parser.add_option("-o", "--outputdir", type="string", default="output",
133 action="store", dest="outputdir", help="output directory (collection) path")
134 parser.add_option("-r", "--outfile", type="string", default="query.txt",
135 action="store", dest="outfile", help="output log file path")
136
137 (options, args) = parser.parse_args()
138 if options.version:
139 print __version__
140 else:
141 # create output dir (collection)
142 output_dir_path = options.outputdir
143 if not os.path.exists(output_dir_path):
144 os.makedirs(output_dir_path)
145
146 querySBT( options, args )
147
148 if __name__ == "__main__": __main__()